The entries we found were just the lucky entries that survived. Why do we find journal entries flying around the wasteland at that farm and the NCR camps? We found what the devs wanted us to find.
As for Horowitz, why would he mention how they go out of the Vault? Its not really an important detail to him at least and I doubt the Courier would be like "wait how did you get out?"
Horowitz and the others were trapped in a section of the Vault that was blocked off from the rest of the Vault. Once we cleared the way, he would have been able to escape through the other door.
Also Chris tells us he got out of the Vault before things went to hell. I doubt the Overseer would just let him go. He was the guy that took care of the reactor and the Overseer didn't let people leave hence the riots. So its possible he left through another door. But yeah I can't rule out the Overseer just letting him go but I think its very unlikely. Again it isn't an important detail to Chris or for the Courier to ask "how did you get out?"
Yeah it would have been nice if the Devs clearly mentioned that there was a secret door, but they did leave enough clues behind for us to figure it out. I can see it being confusing. The wiki messed up the events. It says that the Boomers leaving is what caused the Vault to go to hell and end up like it is in New Vegas. This isn't the case and why I dislike the wiki.